Focus Position Analysis

The purpose of focusing on a specific position of a plate is that it allows to extract detailed -- easily accessible -- information on that colony. This was primary developed as a debug tool.

You need the scan-o-matic_server running

Using python console or ipython:

from scanomatic.models.factories.analysis_factories import AnalysisModelFactory
from scanomatic.io.rpc_client import get_client
m = AnalysisModelFactory.create()
m.output_directory = 'analysis_focal_suppress'
m.compilation = "/your/abs/path/to/data/some_project.project.compilation"
m.suppress_non_focal = True
m.focus_position = (3,1,1)
rc = get_client(admin=True)
rc.create_analysis_job(AnalysisModelFactory.to_dict(m))

Some notes on the above example.

• Any analysis in the output_directory will be overwritten. This does not include previous focus-position data for other positions than the currently selected.
• The path to the compilation file must be absolute.
• It will focus on the position (3, 1, 1) which implies the 4th plate, position {1,1}.
• If suppress_non_focal is set to True, only this position is analysed. This makes the analysis run fast. It will also cause the grid-image to show the focus position rather than the {0,0} position.